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Old post, but this might help others as I had the same question and found the information from Transport Canada over the phone.

You can go to the Transport Canada Website and either License your boat or Register it. My understanding is if you need to register the boat if you plan to cross a boarder, use it commercially or get a marine mortgage. Registration costs $250. Otherwise just get it licensed for free online. I just did this with a boat that bought which had no papers. I know 2 of my buddies also have boats that have never been registered and have lost papers for them. You can actually get a $250 fine for not having either paper work with the boat.